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P

panel - Variable in class HAL.Gui.UIWindow

ParallelFunction - Interface in HAL.Interfaces

ParamSet - Class in HAL.Tools.Internal

the ParamSet class is used to keep track of all of the items in a menu it can be queried to get the current values of the menu values and labels can also be loaded as arrays of strings, allowing for the menuset to be used without a gui

ParamSet() - Constructor for class HAL.Tools.Internal.ParamSet

ParamSet(String[], String[]) - Constructor for class HAL.Tools.Internal.ParamSet

ParamSetChangeAction - Interface in HAL.Interfaces

Created by Rafael on 10/26/2017.

PDEequations - Class in HAL.Tools.Internal

Created by Rafael on 10/14/2017.

PDEequations() - Constructor for class HAL.Tools.Internal.PDEequations

PDEGrid1D - Class in HAL.GridsAndAgents

a 1D

PDEGrid1D(int) - Constructor for class HAL.GridsAndAgents.PDEGrid1D

PDEGrid1D(int, boolean) - Constructor for class HAL.GridsAndAgents.PDEGrid1D

PDEGrid2D - Class in HAL.GridsAndAgents

PDEGrid2D class facilitates 2D diffusion with two arrays of doubles called fields the intended usage is that during a diffusion tick, the current values will be read, and the prev values will be written to after updates, Update is called to set the prev field as the current field.

PDEGrid2D(int, int) - Constructor for class HAL.GridsAndAgents.PDEGrid2D

PDEGrid2D(int, int, boolean, boolean) - Constructor for class HAL.GridsAndAgents.PDEGrid2D

PDEGrid3D - Class in HAL.GridsAndAgents

PDEGrid3D class facilitates 3D diffusion with two arrays of doubles called fields the intended usage is that during a diffusion tick, the current values will be read, and the next values will be written to after updates, Update is called to set the delta field as the current field.

PDEGrid3D(int, int, int) - Constructor for class HAL.GridsAndAgents.PDEGrid3D

PDEGrid3D(int, int, int, boolean, boolean, boolean) - Constructor for class HAL.GridsAndAgents.PDEGrid3D

PhToProtons(double) - Static method in class HAL.Util

converts pH to proton concentration

PhylogenyPop() - Method in class HAL.Tools.PhylogenyTracker.Genome

returns the total population of all living members of the phylogeny

PlanToHistory(int) - Method in class HAL.Tools.InteractiveModel.InteractiveModel

PlotLine - Class in HAL.Gui

this class is used to add segments one at a time to a PlotLine on a UIPlot/PlotWindow

PlotLine(UIPlot, int) - Constructor for class HAL.Gui.PlotLine

establishes the UIPlot that will contain the PlotLine, and the color of the segment lines

PlotLine(double[], double[], int) - Method in class HAL.Gui.UIGrid

plots a line, connecting all pixels between the points defined by the x,y pairs from the xs and ys array with the provided color

PlotLine(double[], double[], int, double) - Method in class HAL.Gui.UIGrid

plots a line, connecting all pixels between the points defined by the x,y pairs from the xs and ys array with the provided color.

PlotLine(double[], double[], int, int, int) - Method in class HAL.Gui.UIGrid

plots a line, connecting all pixels between the points defined by the x,y pairs with the provided color.

PlotLine(double[], double[], int, int, int, double) - Method in class HAL.Gui.UIGrid

plots a line, connecting all pixels between the points defined by the x,y pairs with the provided color.

PlotLine(double[], double[], int, int, int, double, double) - Method in class HAL.Gui.UIGrid

plots a line, connecting all pixels between the points defined by the x,y pairs with the provided color.

PlotLine(double[], int) - Method in class HAL.Gui.UIGrid

plots a line, connecting all pixels between the points defined by the list of x,y,x,y...

PlotLine(double[], int, double) - Method in class HAL.Gui.UIGrid

plots a line, connecting all pixels between the points defined by the list of x,y,x,y...

PlotLine(double[], int, int, int) - Method in class HAL.Gui.UIGrid

plots a line, connecting all pixels between the points defined by the list of x,y,x,y...

PlotLine(double[], int, int, int, double) - Method in class HAL.Gui.UIGrid

plots a line, connecting all pixels between the points defined by the list of x,y,x,y...

PlotLine(double[], int, int, int, double, double) - Method in class HAL.Gui.UIGrid

plots a line, connecting all pixels between the points defined by the list of x,y,x,y...

PlotSegment(double, double, double, double, int) - Method in class HAL.Gui.UIGrid

plots a line segment, connecting all pixels between the points defined by (x1,y1) and (x2,y2) with the provided color.

PlotSegment(double, double, double, double, int, double) - Method in class HAL.Gui.UIGrid

plots a line segment, connecting all pixels between the points defined by (x1,y1) and (x2,y2) with the provided color.

PlotSegment(double, double, double, double, int, double, double) - Method in class HAL.Gui.UIGrid

plots a line segment, connecting all pixels between the points defined by (x1,y1) and (x2,y2) with the provided color.

PlotWindow - Class in HAL.Gui

PlotWindow(int, int) - Constructor for class HAL.Gui.PlotWindow

PlotWindow(int, int, boolean) - Constructor for class HAL.Gui.PlotWindow

PlotWindow(int, int, double, double, double, double) - Constructor for class HAL.Gui.PlotWindow

PlotWindow(int, int, double, double, double, double, boolean) - Constructor for class HAL.Gui.PlotWindow

PlotWindow(int, int, int) - Constructor for class HAL.Gui.PlotWindow

PlotWindow(int, int, int, boolean) - Constructor for class HAL.Gui.PlotWindow

PlotWindow(int, int, int, boolean, GuiCloseAction) - Constructor for class HAL.Gui.PlotWindow

PlotWindow(int, int, int, boolean, GuiCloseAction, boolean) - Constructor for class HAL.Gui.PlotWindow

PlotWindow(int, int, int, double, double, double, double) - Constructor for class HAL.Gui.PlotWindow

PlotWindow(int, int, int, double, double, double, double, boolean) - Constructor for class HAL.Gui.PlotWindow

PlotWindow(int, int, int, double, double, double, double, boolean, GuiCloseAction) - Constructor for class HAL.Gui.PlotWindow

PlotWindow(int, int, int, double, double, double, double, boolean, GuiCloseAction, boolean) - Constructor for class HAL.Gui.PlotWindow

PlotWindow(String, int, int) - Constructor for class HAL.Gui.PlotWindow

PlotWindow(String, int, int, boolean) - Constructor for class HAL.Gui.PlotWindow

PlotWindow(String, int, int, double, double, double, double) - Constructor for class HAL.Gui.PlotWindow

PlotWindow(String, int, int, double, double, double, double, boolean) - Constructor for class HAL.Gui.PlotWindow

PlotWindow(String, int, int, int) - Constructor for class HAL.Gui.PlotWindow

PlotWindow(String, int, int, int, boolean) - Constructor for class HAL.Gui.PlotWindow

PlotWindow(String, int, int, int, boolean, GuiCloseAction) - Constructor for class HAL.Gui.PlotWindow

PlotWindow(String, int, int, int, boolean, GuiCloseAction, boolean) - Constructor for class HAL.Gui.PlotWindow

the PlotWindow object component is similar to the GridWindow object but specifically for generating plots.

PlotWindow(String, int, int, int, double, double, double, double) - Constructor for class HAL.Gui.PlotWindow

PlotWindow(String, int, int, int, double, double, double, double, boolean) - Constructor for class HAL.Gui.PlotWindow

PlotWindow(String, int, int, int, double, double, double, double, boolean, GuiCloseAction) - Constructor for class HAL.Gui.PlotWindow

PlotWindow(String, int, int, int, double, double, double, double, boolean, GuiCloseAction, boolean) - Constructor for class HAL.Gui.PlotWindow

Point1DBool - Interface in HAL.Interfaces

Point2DBool - Interface in HAL.Interfaces

Point3DBool - Interface in HAL.Interfaces

PoissonProb(int, double) - Static method in class HAL.Util

Samples a Poisson distribution

Pop() - Method in class HAL.GridsAndAgents.AgentGrid1D

returns the number of agents that are alive in the grid

Pop() - Method in class HAL.GridsAndAgents.AgentGrid2D

returns the number of agents that are alive in the grid

Pop() - Method in class HAL.GridsAndAgents.AgentGrid3D

returns the number of agents that are alive in the grid

Pop() - Method in class HAL.GridsAndAgents.PopulationGridBase

Pop() - Method in class HAL.GridsAndAgents.PopulationGridLongBase

Pop() - Method in class HAL.Tools.PhylogenyTracker.Genome

returns the current population size that shares this genome

PopAt(int) - Method in class HAL.GridsAndAgents.AgentGrid1D

gets the population at a specific location

PopAt(int) - Method in class HAL.GridsAndAgents.AgentGrid2D

gets the population at a specific location

PopAt(int) - Method in class HAL.GridsAndAgents.AgentGrid3D

gets the population at a specific location

PopAt(int, int) - Method in class HAL.GridsAndAgents.AgentGrid2D

gets the population at a specific location

PopAt(int, int, int) - Method in class HAL.GridsAndAgents.AgentGrid3D

gets the population at a specific location

PopAt(int, int, int, AgentToBool) - Method in class HAL.GridsAndAgents.AgentGrid3D

gets the population at a specific location, subsetting to only those for which EvalAgent returns true

PopAt(int, int, AgentToBool) - Method in class HAL.GridsAndAgents.AgentGrid2D

gets the population at a specific location, subsetting to only those for which EvalAgent returns true

PopAt(int, AgentToBool) - Method in class HAL.GridsAndAgents.AgentGrid1D

gets the population at a specific location, subsetting to only those for which EvalAgent returns true

PopAt(int, AgentToBool) - Method in class HAL.GridsAndAgents.AgentGrid2D

gets the population at a specific location, subsetting to only those for which EvalAgent returns true

PopAt(int, AgentToBool) - Method in class HAL.GridsAndAgents.AgentGrid3D

gets the population at a specific location, subsetting to only those for which EvalAgent returns true

popRemaining - Variable in class HAL.Tools.MultinomialCalc

popRemaining - Variable in class HAL.Tools.MultinomialCalcLong

PopulationGrid1D - Class in HAL.GridsAndAgents

PopulationGrid1D(int) - Constructor for class HAL.GridsAndAgents.PopulationGrid1D

PopulationGrid1D(int, boolean) - Constructor for class HAL.GridsAndAgents.PopulationGrid1D

PopulationGrid1DLong - Class in HAL.GridsAndAgents

PopulationGrid1DLong(int) - Constructor for class HAL.GridsAndAgents.PopulationGrid1DLong

PopulationGrid1DLong(int, boolean) - Constructor for class HAL.GridsAndAgents.PopulationGrid1DLong

PopulationGrid2D - Class in HAL.GridsAndAgents

PopulationGrid2D(int, int) - Constructor for class HAL.GridsAndAgents.PopulationGrid2D

PopulationGrid2D(int, int, boolean, boolean) - Constructor for class HAL.GridsAndAgents.PopulationGrid2D

PopulationGrid2DLong - Class in HAL.GridsAndAgents

PopulationGrid2DLong(int, int) - Constructor for class HAL.GridsAndAgents.PopulationGrid2DLong

PopulationGrid2DLong(int, int, boolean, boolean) - Constructor for class HAL.GridsAndAgents.PopulationGrid2DLong

PopulationGrid3D - Class in HAL.GridsAndAgents

PopulationGrid3D(int, int, int) - Constructor for class HAL.GridsAndAgents.PopulationGrid3D

PopulationGrid3D(int, int, int, boolean, boolean, boolean) - Constructor for class HAL.GridsAndAgents.PopulationGrid3D

PopulationGrid3DLong - Class in HAL.GridsAndAgents

PopulationGrid3DLong(int, int, int) - Constructor for class HAL.GridsAndAgents.PopulationGrid3DLong

PopulationGrid3DLong(int, int, int, boolean, boolean, boolean) - Constructor for class HAL.GridsAndAgents.PopulationGrid3DLong

PopulationGridBase - Class in HAL.GridsAndAgents

PopulationGridBase(int) - Constructor for class HAL.GridsAndAgents.PopulationGridBase

PopulationGridLongBase - Class in HAL.GridsAndAgents

PopulationGridLongBase(int) - Constructor for class HAL.GridsAndAgents.PopulationGridLongBase

PopulationGridPDEequations - Class in HAL.Tools.Internal

PopulationGridPDEequations() - Constructor for class HAL.Tools.Internal.PopulationGridPDEequations

probRemaining - Variable in class HAL.Tools.MultinomialCalc

probRemaining - Variable in class HAL.Tools.MultinomialCalcLong

ProbScale(double, double) - Static method in class HAL.Util

adjusts probability that an event will occur in 1 unit of time to the probability that the event will occur at least once over the duration

ProtonsToPh(double) - Static method in class HAL.Util

converts proton concentration to pH

PWD() - Static method in class HAL.Util

gets the current working directory as a string

Py4jDoublesIn(byte[]) - Static method in class HAL.Util

Py4jDoublesIn(byte[], int) - Static method in class HAL.Util

Py4jDoublesInAsArrayList(byte[], int) - Static method in class HAL.Util

Py4jDoublesOut(double[]) - Static method in class HAL.Util

Py4jDoublesOut(double[][]) - Static method in class HAL.Util

Py4jDoublesOut(ArrayList<double[]>) - Static method in class HAL.Util

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